As the title says. I'm a bit concerned about using both together as there is no control over line pressure.

 

It will work fine.
If you want line pressure control, you can use TransGos vacuum modulator kit.

Depending on the application, fixed line pressure works well.

 

It's for 90%street/10%strip.

 

Application depends on HP, etc.

1000 HP street needs fixed pressure, 400 HP strip doesn't...

 

I'm inclined to ask why you are using a manual controller.
If you have a carb'ed engine and no PCM, I fully understand.
However, often people have incorrect assumptions of what can and cannot be done with a properly/custom tuned PCM.